In the past decade, isolated single atoms have been successfully dispersed on various substrates, with their potential applications being intensively investigated in different reactions. While the essential target of research in single-atom catalysis is the precise synthesis of stable single-atom catalysts (SACs) with clear configurations and impressive catalytic performance, theoretical investigations have also played important roles in identifying active sites, revealing catalytic mechanisms, and establishing structure-activity relationships. Nevertheless, special attention should still be paid in theoretical works to the particularity of SACs. In this Perspective, we will summarize the theoretical progress made on the understanding of the rich phenomena in single-atom catalysis. We focus on the determination of local structures of SACs via comparison between experiments and simulations, the discovery of distinctive catalytic mechanisms induced by multiadsorption, synergetic effects, and dynamic evolutions, to name a few, the proposal of criteria for theoretically designing SACs, and the extension of original concepts of single-atom catalysis. We hope that this Perspective will inspire more in-depth thinking on future theoretical studies of SACs.